/dports/science/p5-Chemistry-Ring/Chemistry-Ring-0.20/t/rings/ |
H A D | mirror.ring | 4 Ring: atoms(a1 a2 a3); bonds(b1 b2 b3); aromatic(0) 5 Ring: atoms(a1 a3 a2); bonds(b3 b2 b1); aromatic(0)
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/dports/science/p5-PerlMol/PerlMol-0.3500/inc/BUNDLES/Chemistry-Ring-0.19/t/rings/ |
H A D | mirror.ring | 4 Ring: atoms(a1 a2 a3); bonds(b1 b2 b3); aromatic(0) 5 Ring: atoms(a1 a3 a2); bonds(b3 b2 b1); aromatic(0)
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/dports/science/p5-Chemistry-File-SMILES/Chemistry-File-SMILES-0.47/ |
H A D | write.pl | 15 unique => $unique, aromatic => $aromatic);
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H A D | SMILES.pm | 479 $opts{aromatic} = 1; # all unique smiles have to be aromatic 485 if ($opts{aromatic}) { 610 return '' if $opts->{aromatic} && $bond->aromatic; 618 $symbol = lc $symbol if $opts->{aromatic} && $atom->aromatic;
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/dports/science/p5-PerlMol/PerlMol-0.3500/inc/BUNDLES/Chemistry-File-SMILES-0.44/ |
H A D | write.pl | 15 unique => $unique, aromatic => $aromatic);
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/dports/science/xdrawchem/xdrawchem-a3f74c34eb09fa72ee16848ec6901049ca5309d5/xdrawchem/ |
H A D | bond.h | 101 bool aromatic() { in aromatic() function 104 if (start->aromatic && end->aromatic) in aromatic()
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/dports/science/rdkit/rdkit-Release_2021_03_5/Contrib/M_Kossner/ |
H A D | BaseFeatures_DIP2_NoMicrospecies.fdef | 20 # aromatic N, but not indole or pyrole or fusing two rings or tetrazole 23 # tertiary nitrogen adjacent to aromatic carbon 29 # Removed aromatic sulfur from ChalcAcceptor definition 30 #We will not use aromatic oxygens! cf Leach, Gillet ... J Med Chem 2010,53, 539-558 91 # guanidine group is positively charged (too promiscuous? We do not match any aromatic systems here… 103 # aromatic rings of various sizes: 109 # match things like 'o1c2cccc2ccc1', which have an aromatic unit spread across multiple simple 150 # 6.2009 (MK): aromatic c is not per se a hydrophobic atom
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/dports/science/p5-PerlMol/PerlMol-0.3500/inc/BUNDLES/Chemistry-Ring-0.19/t/rings2/ |
H A D | norbornane.ring | 3 Ring: atoms(a1 a2 a3 a4 a5); bonds(b1 b2 b3 b4 b5); aromatic(0) 4 Ring: atoms(a1 a2 a3 a6 a7); bonds(b1 b2 b6 b7 b8); aromatic(0)
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H A D | biphenyl.ring | 3 Ring: atoms(a1 a6 a5 a4 a3 a2); bonds(b6 b5 b4 b3 b2 b1); aromatic(1) 4 Ring: atoms(a7 a12 a11 a10 a9 a8); bonds(b13 b12 b11 b10 b9 b8); aromatic(1)
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/dports/science/p5-Chemistry-Ring/Chemistry-Ring-0.20/t/rings2/ |
H A D | norbornane.ring | 3 Ring: atoms(a1 a2 a3 a4 a5); bonds(b1 b2 b3 b4 b5); aromatic(0) 4 Ring: atoms(a1 a2 a3 a6 a7); bonds(b1 b2 b6 b7 b8); aromatic(0)
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H A D | biphenyl.ring | 3 Ring: atoms(a1 a6 a5 a4 a3 a2); bonds(b6 b5 b4 b3 b2 b1); aromatic(1) 4 Ring: atoms(a7 a12 a11 a10 a9 a8); bonds(b13 b12 b11 b10 b9 b8); aromatic(1)
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/dports/science/gromacs/gromacs-2021.4/docs/reference-manual/special/ |
H A D | remove-fast-dgf.rst | 44 planarity mostly deal with aromatic residues. Bonds, angles, and 52 are virtualized, those inside the aromatic residues will be virtualized 53 as well, *i.e.* hydrogens in the aromatic residues are treated 54 differently depending on the treatment of the aromatic residues. Note 55 further that the virtualization of aromatic rings is deprecated. 60 constructions for the aromatic residues are based on the bond lengths 63 construction needed for a whole aromatic group. 115 - *single amine or amide (-NH-) and aromatic hydrogens 161 Out-of-plane vibrations in aromatic groups 164 The planar arrangements in the side chains of the aromatic residues [all …]
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/dports/science/p5-Chemistry-Pattern/Chemistry-Pattern-0.27/Pattern/ |
H A D | Bond.pm | 51 return ($what->order eq $where->order) || ($where->aromatic && $what->aromatic);
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/dports/science/p5-PerlMol/PerlMol-0.3500/inc/BUNDLES/Chemistry-File-SMILES-0.44/t/ |
H A D | names.t | 14 my $out = $mol->print(format => 'smiles', aromatic => 1) . "\t" . $mol->name; 16 $out = $mol->print(format => 'smiles', name => 1, aromatic => 1);
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/dports/science/p5-Chemistry-File-SMILES/Chemistry-File-SMILES-0.47/t/ |
H A D | names.t | 14 my $out = $mol->print(format => 'smiles', aromatic => 1) . "\t" . $mol->name; 16 $out = $mol->print(format => 'smiles', name => 1, aromatic => 1);
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/dports/science/plumed/plumed2-2.7.2/user-doc/tutorials/others/isdb-1/charmm36-eef1sb.ff/ |
H A D | atomtypes.atp | 11 CA 12.01100 ; aromatic C 13 CAI 12.01100 ; aromatic C next to CPT in trp 85 CG2R61 12.01100 ; 6-mem aromatic C 87 CG2R63 12.01100 ; 6-mem aromatic amide carbon (NA) (and other 6-mem aromatic carbonyls?) 89 CG2R66 12.01100 ; 6-mem aromatic carbon bound to F 90 CG2R67 12.01100 ; 6-mem aromatic carbon of biphenyl 125 CN3 12.01100 ; Nucleic acid aromatic carbon 126 CN3T 12.01100 ; Nucleic acid aromatic carbon, Thy C5 163 FGR1 18.99800 ; aromatic fluorine 215 HGR61 1.00800 ; aromatic H [all …]
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/dports/biology/babel/babel-1.6/ |
H A D | tosmiles.c | 227 int aromatic; /* TRUE if ANY of the bonds to it are aromatic */ member 265 initatomdata.aromatic = FALSE; in generatesmilesstring() 288 atomdata[natoms].aromatic = hasaromaticbonds(&frag->atom[atom]); in generatesmilesstring() 426 smileslen += addsmilesatom(tmpstr, atomdata[a].symbol, atomdata[a].aromatic); in generatesmilesstring() 462 smipos += addsmilesatom(&smiles[smipos], atomdata[a].symbol, atomdata[a].aromatic); in generatesmilesstring() 501 addsmilesatom(char *string, char *symbol, int aromatic) in addsmilesatom() argument 517 string[n++] = (aromatic) ? tolower(symbol[0]) : symbol[0]; in addsmilesatom() 521 string[n++] = (aromatic) ? tolower(symbol[1]) : symbol[1]; in addsmilesatom()
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/dports/science/openbabel/openbabel-3.1.1/data/ |
H A D | genheaders.sh | 3 ./bin2hex.pl aromatic.txt AromaticData >aromatic.h
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/dports/science/gromacs/gromacs-2021.4/share/top/amber03.ff/ |
H A D | atomtypes.atp | 4 CA 12.01000 ; sp2 C pure aromatic (benzene) 5 CB 12.01000 ; sp2 aromatic C, 5&6 membered ring junction 6 CC 12.01000 ; sp2 aromatic C, 5 memb. ring HIS 9 CN 12.01000 ; sp2 C aromatic 5&6 memb.ring junct.(TRP)
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/dports/science/gromacs/gromacs-2021.4/share/top/amber99.ff/ |
H A D | atomtypes.atp | 3 CA 12.01000 ; sp2 C pure aromatic (benzene) 4 CB 12.01000 ; sp2 aromatic C, 5&6 membered ring junction 5 CC 12.01000 ; sp2 aromatic C, 5 memb. ring HIS 8 CN 12.01000 ; sp2 C aromatic 5&6 memb.ring junct.(TRP)
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/dports/science/gromacs/gromacs-2021.4/share/top/amber94.ff/ |
H A D | atomtypes.atp | 3 CA 12.01000 ; sp2 C pure aromatic (benzene) 4 CB 12.01000 ; sp2 aromatic C, 5&6 membered ring junction 5 CC 12.01000 ; sp2 aromatic C, 5 memb. ring HIS 8 CN 12.01000 ; sp2 C aromatic 5&6 memb.ring junct.(TRP)
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/dports/science/gromacs/gromacs-2021.4/share/top/amber96.ff/ |
H A D | atomtypes.atp | 3 CA 12.01000 ; sp2 C pure aromatic (benzene) 4 CB 12.01000 ; sp2 aromatic C, 5&6 membered ring junction 5 CC 12.01000 ; sp2 aromatic C, 5 memb. ring HIS 8 CN 12.01000 ; sp2 C aromatic 5&6 memb.ring junct.(TRP)
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/dports/science/gromacs/gromacs-2021.4/share/top/amber99sb.ff/ |
H A D | atomtypes.atp | 3 CA 12.01000 ; sp2 C pure aromatic (benzene) 4 CB 12.01000 ; sp2 aromatic C, 5&6 membered ring junction 5 CC 12.01000 ; sp2 aromatic C, 5 memb. ring HIS 8 CN 12.01000 ; sp2 C aromatic 5&6 memb.ring junct.(TRP)
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/dports/science/gromacs/gromacs-2021.4/share/top/amber99sb-ildn.ff/ |
H A D | atomtypes.atp | 3 CA 12.01000 ; sp2 C pure aromatic (benzene) 4 CB 12.01000 ; sp2 aromatic C, 5&6 membered ring junction 5 CC 12.01000 ; sp2 aromatic C, 5 memb. ring HIS 8 CN 12.01000 ; sp2 C aromatic 5&6 memb.ring junct.(TRP)
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/dports/science/gromacs/gromacs-2021.4/share/top/amberGS.ff/ |
H A D | atomtypes.atp | 3 CA 12.01000 ; sp2 C pure aromatic (benzene) 4 CB 12.01000 ; sp2 aromatic C, 5&6 membered ring junction 5 CC 12.01000 ; sp2 aromatic C, 5 memb. ring HIS 8 CN 12.01000 ; sp2 C aromatic 5&6 memb.ring junct.(TRP)
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